GSM5729873: skate_adult_pelvic_fin_MethylCseq; Leucoraja erinacea; MeDIP-Seq
MethylC-seq library preparation was performed as described previously (PMID: 25692984). Briefly, 1000 ng of genomic DNA extracted from embryonic and adult skate fins was spiked with unmethylated λ phage DNA (Promega) and sonicated to ~300 bp fragments using M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA was then purified, end-repaired using End-It™ DNA End-Repair Kit (Lucigen) and A-tailed using Klenow Fragment (3'→5' exo-) (New England Biolabs) followed by the ligation of NEXTFLEX® Bisulfite-Seq Adapters. Bisulfite conversion of adaptor-ligated DNA was performed using EZ DNA Methylation-Gold Kit (Zymo Research). Library amplification (13 PCR cycles) was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems). Library size was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche) yielding ~10-20 nM.